Identifying the roles of variable individual genetic factors can revolutionize approaches to the diagnosis, treatment, and prevention of human disease. Single nucleotide polymorphisms (SNPs) are the most frequent DNA sequence variations that affect human health, and better methods for scoring known SNPs in the human population are needed. This SBIR project is designed to develop a sensitive, high-throughput, efficient and affordable method of scoring known SNPs. Phase I work and subsequent interim efforts have clearly established the feasibility of our approach. The overall project goal is to develop an advanced electrochemical, peptide nucleic acid (PNA) probe-based array system that can rapidly and reliably measure SNPs. The electrochemical arrays will be developed within the standard microtiter plate format, allowing researchers the ability to adapt their existing automation instrumentation to this more-efficient electrochemical platform. This expanded, 3-year Phase II project will lead to 1) development of specific PNA-based electrochemical sensor assays for the identification/quantification of known SNP sequences; 2) design/fabrication of innovative sensor arrays and appropriate array-reader instrumentation for high-throughput, accurate, easy-to-use, and inexpensive SNPs scoring in human genomic samples; and 3) demonstration, through collaborative studies, of the utility of this approach to SNPs scoring for use by researchers and clinicians. PROPOSED COMMERCIAL APPLICATION: The new SNP scoring system proposed here is rounded on a versatile, automated chip-based system for probe analysis of DNA or RNA. It will serve as a companion instrument to PCR as well as a new tool for direct nucleic acid analysis. The laboratory market for PCR is currently $300 million per year. Our PCR related system would represent a significant new, complementary product in this marketplace. Furthermore, as the clinical market matures, we anticipate a range of diagnostic applications that will increase the opportunities for the instrument.